We propose a dynamic Bayesian model for motifs in biopolymer se- quences which captures rich biological prior knowledge and positional dependencies in motif structure in a principled way. Our model posits that the position-specific multinomial parameters for monomer distribu- tion are distributed as a latent Dirichlet-mixture random variable, and the position-specific Dirichlet component is determined by a hidden Markov process. Model parameters can be fit on training motifs using a vari- ational EM algorithm within an empirical Bayesian framework. Varia- tional inference is also used for detecting hidden motifs. Our model im- proves over previous models that ignore biological priors and positional dependence.

In this paper, we propose a Bayesian framework, which constructs shared-state triphone HMMs based on a variational Bayesian approach, and recognizes speech based on the Bayesian prediction classi(cid:2)cation; variational Bayesian estimation and clustering for speech recognition (VBEC). An appropriate model structure with high recognition perfor- mance can be found within a VBEC framework. Unlike conventional methods, including BIC or MDL criterion based on the maximum likeli- hood approach, the proposed model selection is valid in principle, even when there are insuf(cid:2)cient amounts of data, because it does not use an asymptotic assumption. In isolated word recognition experiments, we show the advantage of VBEC over conventional methods, especially when dealing with small amounts of data.

In recent years variational methods have become a popular tool for approximate inference and learning in a wide variety of proba- bilistic models. For each new application, however, it is currently necessary (cid:12)rst to derive the variational update equations, and then to implement them in application-speci(cid:12)c code. Each of these steps is both time consuming and error prone. In this paper we describe a general purpose inference engine called VIBES ('Variational Infer- ence for Bayesian Networks') which allows a wide variety of proba- bilistic models to be implemented and solved variationally without recourse to coding. New models are speci(cid:12)ed either through a simple script or via a graphical interface analogous to a drawing package.

The Bayesian paradigm provides a natural and effective means of exploit- ing prior knowledge concerning the time-frequency structure of sound signals such as speech and music--something which has often been over- looked in traditional audio signal processing approaches. Here, after con- structing a Bayesian model and prior distributions capable of taking into account the time-frequency characteristics of typical audio waveforms, we apply Markov chain Monte Carlo methods in order to sample from the resultant posterior distribution of interest. We present speech enhance- ment results which compare favourably in objective terms with standard time-varying filtering techniques (and in several cases yield superior per- formance, both objectively and subjectively); moreover, in contrast to such methods, our results are obtained without an assumption of prior knowledge of the noise power.

We argue that human inductive generalization is best explained in a Bayesian framework, rather than by traditional models based on simi- larity computations. We go beyond previous work on Bayesian concept learning by introducing an unsupervised method for constructing flex- ible hypothesis spaces, and we propose a version of the Bayesian Oc- cam's razor that trades off priors and likelihoods to prevent under- or over-generalization in these flexible spaces. We analyze two published data sets on inductive reasoning as well as the results of a new behavioral study that we have carried out.

The application of latent/hidden variable Dynamic Bayesian Net- works is constrained by the complexity of marginalising over latent variables. For this reason either small latent dimensions or Gaus- sian latent conditional tables linearly dependent on past states are typically considered in order that inference is tractable. We suggest an alternative approach in which the latent variables are modelled using deterministic conditional probability tables. This specialisa- tion has the advantage of tractable inference even for highly com- plex non-linear/non-Gaussian visible conditional probability tables. This approach enables the consideration of highly complex latent dynamics whilst retaining the bene(cid:12)ts of a tractable probabilistic model.

Missing data is common in real-world datasets and is a problem for many estimation techniques. We have developed a variational Bayesian method to perform Independent Component Analysis (ICA) on high-dimensional data containing missing entries. Missing data are handled naturally in the Bayesian framework by integrating the generative density model. Mod- eling the distributions of the independent sources with mixture of Gaus- sians allows sources to be estimated with different kurtosis and skewness. The variational Bayesian method automatically determines the dimen- sionality of the data and yields an accurate density model for the ob- served data without overfitting problems.

An essential step in understanding the function of sensory nervous sys- tems is to characterize as accurately as possible the stimulus-response function (SRF) of the neurons that relay and process sensory informa- tion. One increasingly common experimental approach is to present a rapidly varying complex stimulus to the animal while recording the re- sponses of one or more neurons, and then to directly estimate a func- tional transformation of the input that accounts for the neuronal firing. The estimation techniques usually employed, such as Wiener filtering or other correlation-based estimation of the Wiener or Volterra kernels, are equivalent to maximum likelihood estimation in a Gaussian-output-noise regression model. We explore the use of Bayesian evidence-optimization techniques to condition these estimates. We show that by learning hyper- parameters that control the smoothness and sparsity of the transfer func- tion it is possible to improve dramatically the quality of SRF estimates, as measured by their success in predicting responses to novel input.

We present an analysis of concentration-of-expectation phenomena in layered Bayesian networks that use generalized linear models as the local conditional probabilities. This framework encompasses a wide variety of probability distributions, including both discrete and continuous random variables. We utilize ideas from large deviation analysis and the delta method to devise and evaluate a class of approximate inference algo- rithms for layered Bayesian networks that have superior asymptotic error bounds and very fast computation time.

Recent work has examined the estimation of models of stimulus-driven neural activity in which some linear filtering process is followed by a nonlinear, probabilistic spiking stage. We analyze the estimation of one such model for which this nonlinear step is implemented by a noisy, leaky, integrate-and-fire mechanism with a spike-dependent after- current. This model is a biophysically plausible alternative to models with Poisson (memory-less) spiking, and has been shown to effectively reproduce various spiking statistics of neurons in vivo. However, the problem of estimating the model from extracellular spike train data has not been examined in depth. We formulate the problem in terms of max- imum likelihood estimation, and show that the computational problem of maximizing the likelihood is tractable.